News http://www.olex2.org Site News daily 1 2011-05-26T13:12:06Z Olex2 1.2 released http://www.olex2.org/news/Olex2-1.2%20released New features which are available in : Olex2–1.2
chemdraw_thppView of PiM result

Aromatic Rings and metal to π-π interactions visualisation

Extending chemical structure drawing by adding a torus to the aromatic rings (use ChemDraw command to switch the rings on temporarily (e.g. for making pictures), or enable it permanently in the .options file (in the Olex2 installation directory) by adding 'aromatic_rings=true'. Use PiM command to draw the metal to ring's π-π system interactions, alternatively, select the metal and then the atoms of the π-π system before running the command.
NCS beforeNCS after

Symmetry Constraint (olex2.refine)

New non-crystallographic symmetry constraint (if you want to try this for two identical  groups: select any atom in each of the two groups and then type constrain same group 2.

The picture illustrates two overlayed ligands before and after the refinement. After the refinement both ligands adopt average geometry. The number of refined parameters is 297 before and 159 after applying the constraint.

 

Unrestrained refinement

Unrestrained refinement

ADP Ueq restrained to be the same

ADP Ueq similarity applied to  N and adjacent C

ADP volume restrained to be the same

ADP volume similarity applied to  N and adjacent C

New ADP Restraints (olex2.refine)

New restraints to either restrain the Ueq of two atoms to a number, or the Ueq/ADP volume to be similar.

Select the atoms and type

  • restrain adp ueq n to restrain Ueq to be equal to the given number
  • restrain adp ueq to restrain Ueq to be similar for two or more atoms
  • restrain adp volume to restrain the ADP volume to be similar for two or more atoms.

You may need to change the default restraint weight to smaller values (like 0.001 or smaller) to see a visible effect.

 
Contour map view View of the new contour maps, with a colour legend
]]> No publisher oleg 2011-10-06T18:55:00Z News Item Olex2 1.1.5 released http://www.olex2.org/news/olex2-1.1.5-released The new version of Olex2 is released now The new version provides a number of features:
  • tutorials - to help you to start with Olex2
  • olex2-refine - new, fully featured, smtbx based refinement with new angle and dihedral angle restraints and rotated ADP constraint and support for HKLF 5
  • electron density maps for twinned datasets
  • PovRay output including export of polyhedra, planes and iso-surfaces
  • disorder modelling tools (mode fit, mode fit -s, available from the GUI)
  • asymmetric unit reconstruction mode (mode grow -a)
  • better treatment of H atoms for water - the H atoms are constrained and allowed to ride on and rotate around the oxygen atom; coordinated water and R-NH2 are modelled as rotating tetrahedral groups
  • improving inversion function to take into account the space group change like in the case of P31 to P32
  • built in cell search engine - a portable version of LCELLS, fast and efficient way to check if somebody in the lab already collected the dataset
  • extended customisation available including the possibility to permanently restrict the angle to filter hydrogen bonds (hbond_min_angle=120), to restrict Olex2 from removing invalid instructions when reading INS file (preserve_invalid_ins=False) and invert the mouse for zooming (InvertMouse=False) stored in .options file. Other options will be developed for the next release.
  • GUI support for multiple dataset CIFs
  • files can now be read using HTTP links
  • extended atom selection wildcards - use $*,type1,type2 to select all atoms but of specific type
  • CCDC deposition and CheckCif report is available with a click of the button
  • Solvent Accessible Voids calculation is added
]]> No publisher Oleg Dolomanov 2011-09-14T23:00:00Z News Item